DNA metabarcoding - data analysing course - MB120C24
Title: DNA metabarcoding – praktický kurz zpracování dat
Czech title: DNA metabarcoding – praktický kurz zpracování dat
Guaranteed by: Department of Botany (31-120)
Faculty: Faculty of Science
Actual: from 2024
Semester: summer
E-Credits: 2
Examination process: summer s.:
Hours per week, examination: summer s.:0/4, C [DS]
Capacity: 15
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Note: enabled for web enrollment
Guarantor: doc. Mgr. Pavel Škaloud, Ph.D.
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Annotation -
A course focused on the analysis of data obtained by the DNA metabarcoding method (Illumina amplicon sequencing) - from the quality analyses to obtaining abundance tables of individual taxa. The course will consist of both a theoretical and a practical part, where participants will learn how to analyze data using a wide range of bioinformatics tools. The data analysis pipeline will be based on Báilint tools ( https://doi.org/10.1002/ece3.1107 ), and will include quality filtering (FastQC, perl scripts), paired-end assembly (PANDAseq), demultiplexing (fqgrep) clustering ( swarm), chimera detection (usearch), automatic blast (SEED2) and phylogenetic delimitation of taxa (IQtree).
The course is given only in Czech for a better understanding of the methodologies.
Last update: Škaloud Pavel, doc. Mgr., Ph.D. (17.07.2024)